SMTL ID : 4fzb.1 (3 other biounits)

Structure of thymidylate synthase ThyX complexed to a new inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 25 residues within 4Å: Chain A: W.59, R.83, H.84, R.85, S.86, R.178, D.179, H.182, L.186, R.187 Chain C: Q.90, E.91, S.93, R.95 Chain D: S.35, N.36, H.56, K.57, H.58, W.59, S.60, E.63, R.178 Ligands: FAD.2, 0VJ.3 25 PLIP interactions: 9 interactions with chain D, 14 interactions with chain A, 2 interactions with chain C Hydrogen bonds: D:S.35, D:N.36, D:W.59, D:S.60, D:S.60, D:S.60, D:R.178, A:R.83, A:R.83, A:R.85, A:S.86, A:R.178, A:D.179, A:H.182, C:E.91, C:E.91 Salt bridges: D:R.178, A:H.84, A:H.84 pi-Stacking: D:H.58, A:H.182, A:H.182 Hydrophobic interactions: A:L.186 Water bridges: A:S.86, A:S.86 FAD.2: 23 residues within 4Å: Chain A: S.35, N.36, H.56, H.58, W.59, S.60, E.63, R.178 Chain B: Q.90, E.91, S.93 Chain D: W.59, R.83, H.84, R.85, S.86, R.178, D.179, H.182, L.186, R.187 Ligands: FAD.1, 0VJ.8 27 PLIP interactions: 12 interactions with chain D, 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:L.186 Hydrogen bonds: D:R.83, D:R.83, D:S.86, D:R.178, D:D.179, D:H.182, D:R.187, A:S.35, A:N.36, A:H.58, A:S.60, A:S.60, A:S.60, A:R.178, B:E.91, B:E.91 Salt bridges: D:H.84, D:H.84, A:R.178 pi-Stacking: D:H.182, D:H.182, A:H.58 Water bridges: A:K.57, A:K.57, A:W.59 pi-Cation interactions: A:H.58 FAD.6: 24 residues within 4Å: Chain B: W.59, R.83, H.84, R.85, S.86, R.178, D.179, H.182, L.186, R.187 Chain C: S.35, N.36, H.56, K.57, H.58, W.59, S.60, R.178 Chain D: Q.90, E.91, S.93, R.95 Ligands: FAD.9, 0VJ.11 24 PLIP interactions: 14 interactions with chain B, 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:L.186 Hydrogen bonds: B:R.83, B:R.83, B:R.85, B:S.86, B:S.86, B:S.86, B:R.178, B:D.179, B:D.179, C:N.36, C:S.60, C:S.60, C:S.60, C:R.178, D:E.91, D:E.91 Salt bridges: B:H.84, B:H.84, C:R.178 pi-Stacking: B:H.182, B:H.182, C:H.58, C:H.58 FAD.9: 22 residues within 4Å: Chain A: Q.90, E.91, S.93 Chain B: S.35, H.56, K.57, H.58, W.59, S.60, R.178 Chain C: W.59, R.83, H.84, R.85, S.86, R.178, D.179, H.182, L.186, R.187 Ligands: 0VJ.5, FAD.6 22 PLIP interactions: 8 interactions with chain B, 12 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:H.58, B:S.60, B:S.60, B:S.60, B:R.178, C:R.83, C:R.83, C:S.86, C:S.86, C:R.178, C:D.179, C:D.179, A:E.91, A:E.91 Salt bridges: B:R.178, C:H.84, C:H.84 pi-Stacking: B:H.58, C:H.182, C:H.182 pi-Cation interactions: B:H.58 Hydrophobic interactions: C:L.186

4 x 0VJ: 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione(Non-covalent)

0VJ.3: 12 residues within 4Å: Chain A: Q.80, R.83, R.187, G.191, Q.193 Chain C: E.91, F.92, S.93, Q.94, R.95, E.157 Ligands: FAD.1 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:E.91, C:Q.94, C:Q.94, C:E.157, A:Q.193 Hydrogen bonds: C:Q.94, C:R.95, C:E.157, A:R.187, A:R.187 0VJ.5: 12 residues within 4Å: Chain A: E.91, F.92, S.93, Q.94, R.95, E.157 Chain C: Q.80, R.83, R.187, G.191, Q.193 Ligands: FAD.9 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:Q.80, C:Q.193, A:Q.94, A:R.95, A:E.157 Hydrogen bonds: C:R.187, C:R.187, A:Q.94, A:Q.94 0VJ.8: 13 residues within 4Å: Chain B: E.91, F.92, S.93, Q.94, R.95, E.157 Chain D: Q.80, R.83, R.187, G.191, T.192, Q.193 Ligands: FAD.2 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:Q.193, B:Q.94, B:Q.94, B:R.95 Hydrogen bonds: D:R.187, D:R.187, B:Q.94 0VJ.11: 13 residues within 4Å: Chain B: A.79, Q.80, R.83, R.187, G.191, Q.193 Chain D: E.91, F.92, S.93, Q.94, R.95, E.157 Ligands: FAD.6 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:E.91, D:Q.94, D:Q.94, D:R.95, D:E.157, B:R.83 Hydrogen bonds: D:Q.94, D:E.157, B:Q.80, B:R.187, B:R.187

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: Q.90, F.92, T.170, Y.172 Chain B: V.34 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:F.92, A:Y.172 DMS.7: 7 residues within 4Å: Chain B: E.70, Q.90, E.91, F.92, T.170, I.171, Y.172 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:F.92, B:Y.172 DMS.10: 8 residues within 4Å: Chain C: Q.90, E.91, F.92, T.170, Y.172 Chain D: A.31, V.34, S.35 2 PLIP interactions: 2 interactions with chain C pi-Cation interactions: C:F.92, C:Y.172 DMS.12: 7 residues within 4Å: Chain C: V.34, S.35 Chain D: Q.90, E.91, F.92, T.170, Y.172 2 PLIP interactions: 2 interactions with chain D pi-Cation interactions: D:F.92, D:Y.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basta, T. et al., Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Open Biology (2012)

Release Date

2013-05-22

Peptides

Probable thymidylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable thymidylate synthase

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